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ZDOCK Benchmark

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This benchmark is a collection of distinct protein docking test cases. It includes individually crystallized receptor and ligand PDBs and the co-crystallized complex PDBs for testing protein docking algorithms. For detailed information, here is the reference. Please reference Chen R, Mintseris J, Janin J, Weng Z (2003) A Protein-Protein Docking Benchmark, Proteins Proteins 52: 88-91 for the usage of the benchmark.

  • Benchmark 2.0: Featuring 84 test cases: 63 Rigid-body, 13 Medium, and 8 Difficult. Available here.
  • Benchmark 1.0: It includes 59 test cases: 22 enzyme-inhibitor complexes, 19 antibody-antigen complexes, 11 other complexes, and 7 difficult cases. 31 of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme/inhibitor, 5 antibody/antigen, 5 others and 5 difficult. The list of PDB IDs can be found in table 1 of the . To download cleaned-up PDB files, click .
  • Benchmark 0.0: It includes 54 test cases: 22 enzyme-inhibitor complexes, 16 antibody-antigen complexes, 10 other complexes, and 6 difficult cases. 29 of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme/inhibitor, 5 antibody/antigen, 4 others and 4 difficult. The list of PDB IDs can be found . To download cleaned-up PDB files, click .

Protein Engineering